flux.shape.from.one.point.graphics: Plots of flux shape computing from one point
In SimEvolEnzCons: Simulation of Evolution of Enzyme Under Constraints

Description Usage Arguments Details Value See Also Examples

View source: R/flux.shape.from.one.point.graphics.R

Graphics for illustrating results of function flux.shape.from.one.point

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flux.shape.from.one.point.graphics(list_fsfop, N_fun, zoom_delta=NULL,add.eq=TRUE,
gr.s.delta=TRUE,gr.J.E=FALSE,gr.s_cont.E=FALSE,gr.s_disc.E=FALSE,
gr.comp.s=FALSE,gr.tau=FALSE,posi.legend="topleft",...)

`list_fsfop`	Output of the function `flux.shape.from.one.point`
`N_fun`	Numeric. Population size that influence neutral zone
`zoom_delta`	Zoom on axis of apparent mutation effects. See details.
`add.eq`	Logical. Does equilibrium appear on graphics?
`gr.s.delta`	Logical. Add graph of selection coefficient in relation to mutation effect?
`gr.J.E`	Logical. Add graph of flux J in relation to enzyme concentrations?
`gr.s_cont.E, gr.s_disc.E`	Logical. Add graph of selection coefficient (respectively from continuous or discrete expression) in relation to enzyme concentrations?
`gr.comp.s`	Logical. Add graph of comparison of selection coefficient from different expressions (continuous vs discrete)?
`gr.tau`	Logical. Add graph depending on tau?
`posi.legend`	Legend position for activities. See details.
`...`	Arguments to be passed in `plot` function, such as `lwd` or `cex`.

See function flux.shape.from.one.point.

Gives graphics of:

Selection coefficient (discrete expression) in relation to apparent mutation effect δ, which is E^m-E^r (option gr.s.delta)
Flux in relation to mutant concentration E^m (option gr.J.E)
Selection coefficient (continuous expression) in relation to mutant concentration (option gr.s_cont.E)
Selection coefficient (discrete expression) in relation to mutant concentration (option gr.s_disc.E)
Comparison between the two expressions of selection coefficient (option gr.comp.s)
If driving variable τ exists: flux/mutant concentrations/discrete selection coefficient in relation to tau (option gr.tau)

Each enzyme is represented by one color. If there are three enzymes enzymes or less, enzyme 1 is in red, 2 in green and 3 in blue. For more than three enzymes, colors are taken in palette "Spectral" from package 'RColorBrewer'.

Discrete expression of selection coefficient refers to s=(J^m-J^r)/J^r. Available whatever values of enzymes concentrations. See function coef_sel.discrete. Continuous expression of selection coefficient refers to s_i = R_Ei^J delta_i/E_i. Available only for small values of delta_i. See function coef_sel.continue.

The RNV corresponds to enzyme concentrations such as selection coefficient is between -1/N and 1/N.

Zooms

If NULL, default values are applied.

If vector of length 1, symmetry is applied (i.e. -zoom,zoom).

If vector of length 2, zoom values are applied directly.

posi.legend

Indicates coordinates of the upper left corner of the legend. Available only for graph corresponding to gr.s.delta. See more in details of function flux.dome.projections.

Nothing

See function RNV.ranking.order.factor to see against which parameters the RNV depend.